Re: [AMBER] Simulation of complex

From: Dean Cuebas <>
Date: Mon, 19 Apr 2010 11:52:00 -0500

> From: "" <>
> Reply-To: AMBER Mailing List <>
> Date: Mon, 19 Apr 2010 10:42:43 -0500
> To: AMBER Mailing List <>
> Subject: Re: [AMBER] Simulation of complex
> Hi,
> please give us a little more detail on what you actually did, instead of
> what you were trying to do. Many things can go wrong in setting up a
> simulation that come from e.g. naming mismatches. Please provide a list of
> the commands you used, along with the results and error messages this
> gave.
> Working through Amber tutorials B4 and A1 may also help you here...
> Kind Regards,
> Thomas
>> Asfa Ali wrote:
>>> Hi,
>>> I am having a docked complex (from Autodock) of a ligand and DNA. The
>>> docked
>>> file is not recognised by amber, although I am using antechamber to
>>> create
>>> the mol2 and frcmod file of the ligand separately.
>>> Is there any problem with Autodock? Can anyone tell me how to use docked
>>> file from Autodock for simulation in amber?

To use docked ligand from Autodock in MD (all-atom) you need to make
everything all-hydrogens again, since Autodock only uses aromatic and polar
    Save docked ligand coordinates as pdb from Autodock
    Open pdb in YASARA
    Edit -> DELETE-> hydrogens and add back all hydrogens , to get
reasonable hydrogen names. But be careful, the atom names must be unique
and this might not be the case, but Amber NEEDS UNIQUE ATOM NAMES!
So, you might need to fix them to match the atom names in your
ligand.mol2 file that has gaff atom types and charges.
FILE-> Save as-> Pdb file
            Select the NAME in the middle column
            BE SURE TRANSFORM is selected, and Format variant PDB is
selected, and then select the directory and give pdb file a
            NOTE!!!! If transform is not selected, then the coordinates will
NOT be the same as the docked coordinates.

Hope this helps.


>>> I have checked the Amber mailing list but I didn't get any suitable
>>> results.
>>> Kindly help.
>>> Asfa.
>>> _______________________________________________
>>> AMBER mailing list
>> _______________________________________________
>> AMBER mailing list
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
> _______________________________________________
> AMBER mailing list

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Received on Mon Apr 19 2010 - 10:00:03 PDT
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